Python library for single-cell TCR analysis
Project description
Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization.
Getting started
Please refer to the documentation. In particular, the
Tutorial, and the
In the documentation, you can also learn more about our T-cell receptor model.
Case-study
The case study from our preprint is available here.
Installation
You need to have Python 3.6 or newer installed on your system. If you don’t have Python installed, we recommend installing Miniconda.
Install the latest release of scirpy from PyPI:
pip install scirpyOr, get it from Bioconda:
conda install -c conda-forge -c bioconda scirpyAlternatively, install the latest development version:
pip install git+https://github.com/icbi-lab/scirpy.git@masterRelease notes
See the release section.
Contact
Please use the issue tracker.
Citation
Sturm, G. Tamas, GS, …, Finotello, F. (2020). Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data. Bioinformatics. doi:10.1093/bioinformatics/btaa611
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